In this study the green method for synthesizing selenium nanoparticles (SeNPs) is experienced, in which the leaf extract of Adiantum capillus was used as an effective chelating and capping agent for producing SeNPs. The characterization techniques that achieved to confirm the synthesis and the structure details of the SeNPs were: UV–Vis spectroscopy, FT-IR analysis, XRD, EDX and SEM analysis. The biological activity of the synthesized SeNPs were tested and compared to the crude extract of Adiantum capillus on gentamicin model of nephrotoxicity in Wistar rats. Sera were used to test the pro-inflammatory cytokines Tumor necrosis factor alpha (TNF-α) and Interleukin beta (IL-β) levels. Histopathology and immunohistochemistry analysis for the apoptosis regulator protein (Bcl-2) and the interstitial filament protein (Vimentin) were performed. Results revealed that the synthesized SeNPs peak appeared at 400–430 nm wave length with crystallite particle size is around 37 nm. The predominant shape is spherical and cubic at different magnification levels with a narrow size distribution of 22.04–128.43 nm. The synthesized SeNPs showed a strong protective effect against gentamicin induced toxic effects to the rat’s kidneys obtained from the (kidney function parameters, histopathology evaluation, recovery of the pro-inflammatory cytokines IL-β and TNF-α level with retrieval of Bcl-2 and vimentin protein levels proximate to the vehicle control groups). Due to the significant protective effect of SeNPs, it considered much better than the crude extract of Adiantum capillus in the treatment of kidney injury; however, additional studies are necessary to find the precise mechanism of their action.